The accurate prediction of building indoor overheating risk is critical in order to mitigate its possible consequences on occupant health and wellbeing. The Chartered Institution of Building Services Engineers issued Technical Memorandum 59 (TM59) with the aim of achieving consistency in the modelling processes followed for the prediction of overheating risk in new dwellings. However, as each tool’s prediction may depend on its inherent assumptions, an inter-model comparison procedure was used to assess whether the choice of building performance simulation tool influences the overheating assessment. The predictions of two popular tools, IES VE and EnergyPlus, were compared for nine variations of a naturally ventilated, purpose built, London flat archetype, modelled under the default algorithm options. EnergyPlus predicted a high overheating risk according to TM59 criteria in seven out of the nine model variants, contrary to the low risk of all the IES VE variants. Analysis of heat transfer processes revealed that wind-driven ventilation and surface convection algorithms were the main sources of the observed discrepancies. The choice of simulation tool could thus influence the overheating risk assessment in flats, while the observed discrepancies in the simulation of air and heat transfer could have implications on other modelling applications. Practical application:Technical Memorandum 59 issued by the Chartered Institution of Building Services Engineers may be widely adopted within the industry to assist the prediction of overheating risk in new dwellings. This work suggests that the choice of building performance simulation tool can greatly influence the predicted overheating risk. Furthermore, the differences identified in the modelling of heat transfer processes could also impact other modelling applications. Following these results, the need for detailed empirical validation studies of naturally ventilated homes has been highlighted.